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Detailed information for vg0420329083:

Variant ID: vg0420329083 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 20329083
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.10, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


CGCTTCTCTTCTTGAAGACGTCGTTTTGGTATACCCTAGGGGGCGATCTCGGCTGTGTCCCTTTGTTGGTCTAGTGGCAGCCGGTCACGCTTAGCGGCGG[T/C]
CGGTCCGGTGCTAGCCTTTTCTTGGGCTTGTGTGTTGGCGATGTCGGTATGTGGGTGGTGGTATTTTTTTCCTTTTTCTTGGTTATGACCCTCCAAGGTT

Reverse complement sequence

AACCTTGGAGGGTCATAACCAAGAAAAAGGAAAAAAATACCACCACCCACATACCGACATCGCCAACACACAAGCCCAAGAAAAGGCTAGCACCGGACCG[A/G]
CCGCCGCTAAGCGTGACCGGCTGCCACTAGACCAACAAAGGGACACAGCCGAGATCGCCCCCTAGGGTATACCAAAACGACGTCTTCAAGAAGAGAAGCG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 75.20% 24.80% 0.00% 0.00% NA
All Indica  2759 98.30% 1.70% 0.00% 0.00% NA
All Japonica  1512 30.40% 69.60% 0.00% 0.00% NA
Aus  269 85.90% 14.10% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 95.70% 4.30% 0.00% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 97.70% 2.30% 0.00% 0.00% NA
Temperate Japonica  767 3.90% 96.10% 0.00% 0.00% NA
Tropical Japonica  504 65.50% 34.50% 0.00% 0.00% NA
Japonica Intermediate  241 41.50% 58.50% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 65.60% 34.40% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0420329083 T -> C LOC_Os04g33580.1 downstream_gene_variant ; 679.0bp to feature; MODIFIER silent_mutation Average:44.982; most accessible tissue: Zhenshan97 flag leaf, score: 63.101 N N N N
vg0420329083 T -> C LOC_Os04g33580-LOC_Os04g33590 intergenic_region ; MODIFIER silent_mutation Average:44.982; most accessible tissue: Zhenshan97 flag leaf, score: 63.101 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0420329083 NA 4.04E-06 mr1183 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420329083 NA 2.72E-07 mr1277 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420329083 NA 1.55E-21 mr1698 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420329083 NA 1.10E-09 mr1277_2 Jap_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420329083 NA 1.46E-21 mr1698_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251